Breast cancer
|
|
|
|
Ding et al.1717 Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 2010; 464(7291):999-1005.
|
1 |
All |
WGS and/or exome sequencing |
Yost et al.1818 Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, et al. Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res. 2012; 40(14):e107.
|
2 |
All |
WGS and/or exome sequencing |
Nik-Zainal et al.1919 Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K, et al; Breast Cancer Working Group of the International Cancer Genome Consortium. Mutational processes molding the genomes of 21 breast cancers. Cell. 2012; 149(5):979-93.
|
21 |
All |
WGS and/or exome sequencing |
Banerji et al.2020 Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012; 486(7403):405-9.
|
103 |
All |
WGS and/or exome sequencing |
Shah et al.2121 Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012; 486(7403):395-9.
|
63 |
All |
WGS and/or exome sequencing |
Stephens et al.2222 Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012; 486(7403):400-4.
|
100 |
All |
WGS and/or exome sequencing |
Ellis et al.2323 Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012; 486(7403):353-60.
|
317 |
All |
WGS and/or exome sequencing (77 patients), PIK3CA, TP53, CDHIand GATA3(240 patients) |
Jiao et al.2424 Jiao X, Hooper SD, Djureinovic T, Larsson C, Wärnberg F, Tellgren-Roth C, et al. Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing. BMC Genomics. 2013; 14:165.
|
15 |
All |
WGS and/or exome sequencing |
Craig et al.2525 Craig DW, O'Shaughnessy JA, Kiefer JA, Aldrich J, Sinari S, Moses TM, et al. Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities. Mol Cancer Ther. 2013; 12(1):104-16.
|
14 |
All |
WGS and/or exome sequencing |
Benvenuti et al.2626 Benvenuti S, Frattini M, Arena S, Zanon C, Cappelletti V, Coradini D, et al. PIK3CA cancer mutations display gender and tissue specificity patterns. Hum Mutat. 2008; 29(2):284-8.
|
85 |
PIK3CA
|
Direct sequencing |
Miron et al.2727 Miron A, Varadi M, Carrasco D, Li H, Luongo L, Kim HJ, et al. PIK3CA mutations in in situ and invasive breast carcinomas. Cancer Res. 2010; 70(14):5674-8.
|
80 |
PIK3CA
|
Direct sequencing |
Martins et al.2828 Martins FC, De S, Almendro V, Gönen M, Park SY, Blum JL, et al. Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discov. 2012; 2(6):503-11.
|
75 |
PIK3CA
|
Direct sequencing |
Hernandez et al.2929 Hernandez L, Wilkerson PM, Lambros MB, Campion-Flora A, Rodrigues DN, Gauthier A, et al. Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra-tumour genetic heterogeneity and clonal selection. J Pathol. 2012; 227(1):42-52.
|
13 |
PIK3CA
|
Sequenom MassArray – direct sequencing |
Lima et al.3030 Lima EU, Soares IC, Danilovic DL, Marui S. New mutation in the PTEN gene in a Brazilian patient with Cowden's syndrome. Arq Bras Endocrinol Metabol. 2012; 56(8):592-6.
|
1 |
PTEN
|
Direct sequencing |
Jong et al.3131 Jong YJ, Li LH, Tsou MH, Chen YJ, Cheng SH, Wang-Wuu S, et al. Chromosomal comparative genomic hybridization abnormalities in early- and late-onset human breast cancers: correlation with disease progression and TP53 mutations. Cancer Genet Cytogenet. 2004; 148(1):55-65.
|
89 |
TP53
|
DHPLC – direct sequencing |
Lavarino et al.3232 Lavarino C, Corletto V, Mezzelani A, Della Torre G, Bartoli C, Riva C, et al. Detection of TP53 mutation, loss of heterozygosity and DNA content in fine-needle aspirates of breast carcinoma. Br J Cancer. 1998; 77(1):125-30.
|
31 |
TP53
|
SSCP – direct sequencing |
Wistuba et al.3333 Wistuba II, Tomlinson GE, Behrens C, Virmani A, Geradts J, Blum JL, et al. Two identical triplet sisters carrying a germline BRCA1 gene mutation acquire very similar breast cancer somatic mutations at multiple other sites throughout the genome. Genes Chromosomes Cancer. 2000; 28(4):359-69.
|
2 |
TP53
|
SSCP – direct sequencing |
Masri et al.3434 Masri MA, Abdel Seed NM, Fahal AH, Romano M, Baralle F, El Hassam AM, et al. Minor role for BRCA2 (exon11) and P53 (exon 5-9) among Sudanese breast cancer patients. Breast Cancer Res Treat. 2002; 71(2):145-7.
|
19 |
TP53
|
Direct sequencing |
Lien et al.3535 Lien HC, Lin CW, Mao TL, Kuo SH, Hsiao CH, Huang CS. P53 overexpression and mutation in metaplastic carcinoma of the breast: genetic evidence for a monoclonal origin of both the carcinomatous and the heterogeneous sarcomatous components. J Pathol. 2004; 204(2):131-9.
|
14 |
TP53
|
Direct sequencing |
Eachkoti et al.3636 Eachkoti R, Hussain I, Afroze D, Aejazaziz S, Jan M, Shah ZA, et al. BRCA1 and TP53 mutation spectrum of breast carcinoma in an ethnic population of Kashmir, an emerging high-risk area. Cancer Lett. 2007; 248(2):308-20.
|
25 |
TP53
|
SSCP – direct sequencing |
Vincent-Salomon et al.3737 Vincent-Salomon A, Gruel N, Lucchesi C, MacGrogan G, Dendale R, Sigal-Zafrani B, et al. Identification of typical medullary breast carcinoma as a genomic sub-group of basal-like carcinomas, a heterogeneous new molecular entity. Breast Cancer Res. 2007; 9(2):R24.
|
48 |
TP53
|
Direct sequencing |
Aceto et al.3838 Aceto GM, Solano AR, Neuman MI, Veschi S, Morgano A, Malatesta S, et al. High-risk human papilloma virus infection, tumor pathophenotypes, and BRCA1/2 and TP53 status in juvenile breast cancer. Breast Cancer Res Treat. 2010; 122(3):671-83.
|
4 |
TP53
|
SSCP – direct sequencing |
Curtis et al.3939 Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012; 486(7403):346-52.
|
820 |
TP53
|
Direct sequencing |
Ripamonti et al.4040 Ripamonti CB, Colombo M, Mondini P, Siranoush M, Peissel B, Bernard L, et al. First description of an acinic cell carcinoma of the breast in a BRCA1 mutation carrier: a case report. BMC Cancer. 2013; 13:46.
|
1 |
TP53
|
Direct sequencing |
Sjoblom et al.4141 Sjöblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, et al. The consensus coding sequences of human breast and colorectal cancers. Science. 2006; 314(5797):268-74.
|
36 |
TP53/GATA3/CDHI
|
Direct sequencing |
Ang et al.4242 Ang D, VanSandt AM, Beadling C, Warrick A, West RB, Corless CL, et al. Biphasic papillary and lobular breast carcinoma with PIK3CA and IDH1 mutations. Diagn Mol Pathol. 2012; 21(4):221-4.
|
1 |
TP53/PIK3CA
|
Sequenom MassArray – direct sequencing |
Serous ovarian cancer
|
|
|
|
Bell et al.4343 Bell D, Berchuck A, Birrer M, Chien J, Chamer D, Dao F, et al. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011; 474(7353):609-15.
|
309 |
All |
WGS and/or exome sequencing |
Jones et al.4444 Jones S, Wang TL, Kurman RJ, Nakayama K, Velculescu VE, Vogelstein B, et al. Low-grade serous carcinomas of the ovary contain very few point mutations. J Pathol. 2012; 226(3):413-20.
|
17 |
All |
WGS and/or exome sequencing (8 patients) and direct sequencing (KRAS– 9 patients) |
Zhang et al.4545 Zhang J, Shi Y, Lalonde E, Li L, Cavallone L, Ferenczy A, et al. Exome profiling of primary, metastatic and recurrent ovarian carcinomas in a BRCA1-positive patient. BMC Cancer. 2013; 13:146.
|
1 |
All |
WGS and/or exome sequencing |
Bashashati et al.4646 Bashashati A, Ha G, Tone A, Ding J, Prentice LM, Roth A, et al. Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling. J Pathol. 2013; 231(1):21-34.
|
5 |
All |
WGS and/or exome sequencing |
Merajver et al.4747 Merajver SD, Pham TM, Caduff RF, Chen M, Poy EL, Cooney KA, et al. Somatic mutations in the BRCA1 gene in sporadic ovarian tumours. Nat Genet. 1995; 9(4):439-43.
|
15 |
BRCAl
|
SSCP – direct sequencing |
Koul et al.4848 Koul A, Loman N, Malander S, Borg A, Ridderheim M. Two BRCA1-positive epithelial ovarian tumors with metastases to the central nervous system: a case report. Gynecol Oncol. 2001; 80(3):399-402.
|
2 |
BRCAl
|
PTT – SPSS – direct sequencing |
Enomoto et al.4949 Enomoto T, Weghorst CM, Inoue M, Tanizawa O, Rice JM. K-ras activation occurs frequently in mucinous adenocarcinomas and rarely in other common epithelial tumors of the human ovary. Am J Pathol. 1991; 39(4):777-85.
|
10 |
KRAS
|
Direct sequencing |
Fu et al.5050 Fu S, Hennessy BT, Ng CS, Ju Z, Coombes KR, Wolf JK, et al. Perifosine plus docetaxel in patients with platinum and taxane resistant or refractory high-grade epithelial ovarian cancer. Gynecol Oncol. 2012; 126(1):47-53.
|
10 |
KRAS
|
Direct sequencing |
Mandai et al.5151 Mandai M, Konishi I, Komatsu T, Mori T, Arao S, Nomura H, et al. Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression. Br J Cancer. 1995; 72(3):691-5.
|
21 |
KRAS
|
SSCP – direct sequencing |
Otsuka et al.5252 Otsuka J, Okuda T, Sekizawa A, Amemiya S, Saito H, Okai T, et al. M. Detection of P53 mutations in the plasma DNA of patients with ovarian cancer. Int J Gynecol Cancer. 2004; 14(3):459-64.
|
14 |
TP53
|
SSCP – direct sequencing |
Kringen et al.5353 Kringen P, Wang Y, Dumeaux V, Nesland JM, Kristensen G, Borresen-Dale AL, et al. TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival. BMC Cancer. 2005; 5:134.
|
24 |
TP53
|
TTGE – direct sequencing |
Dehari et al.5454 Dehari R, Kurman RJ, Logani S, Shih IM. The development of high-grade serous carcinoma from atypical proliferative (borderline) serous tumors and low-grade micropapillary serous carcinoma: a morphologic and molecular genetic analysis. Am J Surg Pathol. 2007; 31(7):1007-12.
|
6 |
TP53/KRAS
|
Direct sequencing |
Birch et al.5555 Birch AH, Arcand SL, Oros KK, Rahimi K, Watters AK, Provencher D, et al. Chromosome 3 anomalies investigated by genome wide SNP analysis of benign, low malignant potential and low grade ovarian serous tumours. PLoS One. 2011; 6(12):e28250.
|
10 |
TP53/KRAS
|
Direct sequencing |
Wojnaeowicz et al.5656 Wojnarowicz PM, Oros KK, Quinn MC, Arcand SL, Gambaro K, Madore J, et al. The genomic landscape of TP53 and P53 annotated high grade ovarian serous carcinomas from a defined founder population associated with patient outcome. PLoS One. 2012; 7(9):e45484.
|
95 |
TP53/KRAS
|
Direct sequencing |
Sangha et al.5757 Sangha N, Wu R, Kuick R, Powers S, Mu D, Fiander D, et al. Neurofibromin 1 (NF1) defects are common in human ovarian serous carcinomas and co-occur with TP53 mutations. Neoplasia. 2008; 10(12):1362-72.
|
41 |
TP53/KRAS/NF1
|
PTT – direct sequencing |
Kinde et al.5858 Kinde I, Bettegowda C, Wang Y, Wu J, Agrawal N, Shih IM, et al. Evaluation of DNA from the Papanicolaou test to detect ovarian and endometrial cancers. Sci Transl Med. 2013; 5(167):167ra4.
|
18 |
TP53/KRAS/NF1
|
Direct sequencing |